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Not sure why you were using step when you could be using the specialized archive step, but either should work the same, just a matter of style.
It sounds like there are two issues here.
First of all, ArtifactUnarchiverStepExecution.copy does not appear to handle symlinks as written. This should be filed as a separate bug, especially if you can find a quick way to reproduce on a minimal test case. I suspect the best that can be done against current Jenkins core versions is to skip over symlinks (emitting a warning from the step); VirtualFile can be asked isFile, which I think would be false for a symlink (even if its target was an existing file), but it would require a core API change for it to report the target of the symlink.
Second, as you say the whole agent/dist/ subdirectory should never have been archived to begin with. I suspect something wrong with your include/exclude patterns, which ought to be reproducible in a freestyle project with the same workspace contents and an archiving post-build action. Try exclude: 'agent/dist/' rather than exclude: 'agent/dist/**/*'; they may seem synonymous but the behavior (implemented in Ant) might be different where symlinks are concerned. (agent/dist/ is merely shorthand for agent/dist/**, meaning “anything starting with agent/dist/, so prune at agent/dist”. agent/dist/**/* means “look through all subdirectories of agent/dist and match all individual files you find in them”.)
Also rather than
I would use